Qiao Liu – Curriculum Vitae

Address James H. Clark Center Mobile Phone (+1)6502835489 Stanford, CA, 94305 (+86)18810226334 Website http://liuqiao.me/ Email [email protected]

Research Statement

My research interests cover problems on statistical learning and computational biology problems. In particular, I am interested in developing machine learning algorithms, especially deep learning algorithms with applications in both general statistics and specific problems in computational biology, pharmacopathology, and health care. Related related works have been published in top journals (PNAS, Nature Machine Intelligence, Bioinformatics) and conferences (ISMB 19’, ECCB 20’, NeurIPS 20’, MICCAI 20’).

Education

2019.09- Joint Ph.D. student - Stanford University, Stanford, USA Present Department of Statistics, advised by Prof. Wing Hung Wong (NAS member) Developing machine learning algorithms with applications in both general statistics and biomedical data

2016.09- Ph.D. candidate in Control Science and Engineering - Tsinghua University, Beijing, China 2021.06 Department of Automation, advised by tenured Assoc. Prof. Rui Jiang Tsinghua National Laboratory for Informatics and Technology (TNLIST)

2015.08- Exchange Student - Lund University, Lund, Sweden 2016.01 Department of Computer Science GPA:5.0/5.0

2012.09- Bachelor in Engineering - Beihang University, Beijing, China 2016.06 ShenYuan Honors College (Special Pilot Class, formerly a.k.a. School of Advanced Engineering) GPA:91.5/100, Rank:2/50

Internships

2019.06- Research Intern - SenseTime Inc, Beijing, China 2019.09 AI+Healthcare, mentored by Dr. Mu Zhou Developing ML algorithms for drug sensitivity prediction and novel drug discovery

2015.09- Undergraduate Intern - LUGG Lab, Lund, Sweden 2015.12 Lund University Graphics Group, advised by Assoc. Prof. Michael Doggett Developing and maintaining RenderChimp graphics applications platform

Publications

1. Qiao Liu, Jiaze Xu, Rui Jiang, Wing Hung Wong. Density estimation with deep generatative neural networks [J]. Proceedings of the National Academy of Sciences of the United States of America(PNAS), 2021, 118(15), e2101344118.

2. Qiao Liu, Shengquan Chen, Rui Jiang, Wing Hung Wong. Simultaneous deep generative modeling and clus- tering of single cell genomic data[J]. Nature Machine Intelligence, 2021, 3(6): 536-544.

1 of 4 3. Qiao Liu, Kui Hua, Xuegong Zhang, Wing Hung Wong, Rui Jiang. Incorporating gene expression in genome- wide prediction of chromatin accessibility via deep learning[J]. Genomics, Proteomics & Bioinformatics, 2021. (In press) 4. Chencheng Xu, Qiao Liu, Minlie Huang, Tao Jiang. Reinforced molecular optimization with neighborhood- controlled grammars[C]. Conference on Neural Information Processing Systems (NeurIPS), 2020, 33. (Top machine learning conf, acceptance rate:20.1%) 5. Kexin Ding, Qiao Liu, Edward Lee, Mu Zhou, Aidong Lu, Shaoting Zhang. Feature-enhanced graph networks for genetic mutational prediction using histopathological images in colon cancer[C]. International Confer- ence on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2020, (pp. 294-304). (Top medical image conf) 6. Qiao Liu, Zhiqiang Hu, Rui Jiang, Mu Zhou. Cancer drug response prediction via a hybrid graph convolu- tional network[J]. Bioinformatics, 2020. 36(Supplement_2): i911-i918. Also in Proceedings of the 19th Euro- pean Conference on Computational Biology (ECCB), 2020.(Top bioinformatics conf, conference acceptance rate:20.2%) 7. Chencheng Xu, Qiao Liu, Jianyu Zhou, Minzhu Xie, Jianxing Feng, Tao Jiang. Quantifying functional impacts of regulatory variants with multi-task Bayesian neural network[J]. Bioinformatics, 2020, 36(5): 1397-1404. (Top bioinformatics journal, JCR Q1) 8. Qingzhu Yang, Qiao Liu, Hairong Lv. A Decentralized System for Medical Data Management via Blockchain [J]. Journal of Internet Technology, 2020, 21(5): 1335-1345. 9. Junfeng Liu, Qiao Liu, Qingzhu Yang. Mstree: a multispecies coalescent approach for estimating ancestral population size and divergence time during speciation with gene flow [J]. Genome biology and evolution, 2020, 12(5): 715-719. (JCR Q2) 10. Qiao Liu, Hairong Lv, Rui Jiang. hicGAN infers super resolution Hi-C data with generative adversarial net- works. Bioinformatics, 2019, 35(14): i99-i107. Also in Proceedings of the 27th Intelligent Systems for Molecu- lar Biologythe 18th European Conference on Computational Biology (ISMB/ECCB), 2019. (Top bioinformatics conf, conference acceptance rate:18.9%) 11. Pengyu Chen*, Qiao Liu*, Lan Wei, Beier Zhao, Yin Jia, Hairong Lv, Xiaolu Fei. Automatically structuring on Chinese ultrasound report of cerebrovascular diseases via natural language processing[J]. IEEE Access, 2019, 7: 89043-89050. (Co-first author, JCR Q1) 12. Shaoming Song, Hongfei Cui, Shengquan Chen, Qiao Liu, Rui Jiang. EpiFIT: Functional interpretation of tran- scription factors based on combination of sequence and epigenetic information[J]. Quantitative Biology, 2019, 1-11. 13. Qijin Yin, Mengmeng Wu, Qiao Liu, Rui Jiang. DeepHistone: a deep learning approach to predicting histone modifications[J]. BMC Genomics, 2019,20(2):193. (JCR Q2) 14. Qiao Liu, Fei Xia, Qijin Yin, Rui Jiang. Chromatin accessibility prediction via a hybrid deep convolutional neural network[J]. Bioinformatics, 2017, 34(5): 732-738. (Top bioinformatics journal, JCR Q1) 15. Qiao Liu, Mingxin Gan, Rui Jiang. A sequence-based method to predict the impact of regulatory variants using random forest[J]. BMC Systems Biology, 2017, 11(2): 7. (JCR Q2) Also in Proceedings of the 15th Asia Pacific Bioinformatics Conference (APBC), 2017. 16. Bai Li, Mu Lin, Qiao Liu, Ya Li, Changjun Zhou. Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm[J]. Journal of Molecular Modeling, 2015, 21(10): 261. (JCR Q2) (* denotes equal contribution)

Invited Talks

2020.09 ECCB 2020(The 19th European Conference on Computational Biology), Virtual talk due to COVID-19. 2020.03 CEGS GGR(Centers of Excellence in Genomic Science Seminar), Stanford University, USA. 2019.11 BIBM 2019(2019 IEEE International Conference on Bioinformatics & Biomedicine), San Diego, USA 2019.07 ISMB 2019(The 27th Conference on Intellegent Systems for Molecular Biology), Basel, Switzerland 2019.03 BUAFAI 2019(The First Beijing Universities Academic Forum of Artificial Intelligence), Beijing, China 2017.01 APBC 2017(The Fifteenth Asia Pacific Bioinformatics Conference), Shenzhen, China

2 of 4 Honers and Awards

2021.06 Excellent Ph.D. Thesis, Tsinghua University (6% of all Ph.D. theses) 2021.06 Excellent Graduates of Tsinghua University, Tsinghua University (5% of all graduate students) 2021.06 Excellent Graduates of Beijing, Beijing Municipal Commission of Education (5% of all graduate students) 2020.10 Friends of Tsinghua - Mingwei Zhang Scholarship, Tsinghua University 2020.08 ECCB Fellowship, International Society for Computational Biology 2019.10 The First Class Scholarship, Tsinghua University 2019.07 CSC Scholarship, China Scholarship Council 2019.04 ISMB Travel Fellowship, International Society for Computational Biology 2018.10 National Scholarship, Ministry of Education of China (7 out of all Ph.D. students in Department of Automation, Tsinghua University) 2017.10 The First Class Scholarship, Tsinghua University 2016.06 Excellent Graduates of Beijing, Beijing Municipal Commission of Education 2016.06 Excellent Graduates of Beihang University, Beihang University () 2016.05 Rui An First Prize Scholarship, Rui An Inc 2015.10 National Encouragement Scholarship, Ministry of Education of China 2015.06 Microsoft Young Fellowship, Microsoft Research Asia (40 undergraduates among top universities in China) 2014.10 National Encouragement Scholarship, Ministry of Education of China 2013.10 National Encouragement Scholarship, Ministry of Education of China 2012.09 Excellent Freshman Prize, Beihang University

Competitions

2021.05 RNA Unpaired Probability Prediction Competition, rank:3/1012, Baidu AI Studio, DCIC 2019 2019.03 Liver Cancer Image Diagnose Competition, rank:2/1397, Digital China Innovation Contest, DCIC 2019 2015.01 Honorable Mention in COMAP’s Mathematical Contest in Modeling, The American Mathematical Society 2014.10 1st Prize in NCSMC(The 6th National College Students Mathematical Competition), Chinese Mathematical Society 2014.09 National 1st Prize in CUMCM(Contemporary Undergraduate Mathematical Contest in Modeling), China Society for Industrial and Applied Mathematics 2014.09 1st Prize in Mathematical Competition, Beihang University 2013.12 1st Prize in Physical Competition, Beihang University 2013.10 1st Prize in NCSMC(The 5th National College Students Mathematical Competition), Chinese Mathematical Society

Technical Strengths

Programming Languages Python,C,Shell,R,Matlab

Deep learning software stacks TensorFlow,Keras,PyTorch,PyTorch Lightning,Theano

Miscellaneous Git,OpenMP,Slurm,Flask,Apache Web Servers

Teaching Experiences

2019.02- Teaching Assistant, Fundamental Industry Training Center, Tsinghua University 2019.06 Smart Things and Intelligent Systems, Undergraduate Course

3 of 4 2018.09- Teaching Assistant, Department of Automation, Tsinghua University 2019.01 Introduction to Artificial Intelligence, Undergraduate Course

2017.09- Teaching Assistant, Department of Automation, Tsinghua University 2018.01 Introduction to Artificial Intelligence, Undergraduate Course

2016.08- Teaching Assistant, Department of Automation, Tsinghua University 2016.09 Project of Electronic Circuits, Undergraduate Summer Course

Professional Activities

Member of International Society of Computational Biology (ISCB). Student member of Institute of Electrical and Electronics Engineers (IEEE). Independent Reviewer for Journals: Nature Machine Intelligence, Bioinformatics, BMC Genomics, Computational Biology and Bioinformatics Independent Reviewer for Conferences: GIW 2018, ISB2018, IDASB2018, BECB2021

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